Evolution of Labeo victorianus predates the Pleistocene desiccation of Lake Victoria: evidence from mitochondrial DNA sequence variation

Geological data show that Lake Victoria dried out some 15 000 years ago. These data suggest that the entire faunal diversity within the lake has evolved since this time. However, mitochondrial DNA sequence diversity in the endemic cyprinid fish, Labeo victorianus, was high (24 haplotypes in 38 individuals; percentage sequence divergence of 0.74%), suggesting that the evolution of this species predates this Late Pleistocene climatological event. This finding is consistent with what has been reported earlier for cichlid fishes in the lake

Population morphological variation of the Nile perch (Lates niloticus, L. 1758), of East African Lakes and their associated waters

In this study an attempt was made to determine whether there are morphological variations associated with the different geographical populations of the Nile perch of East Africa. Analyses of the levels of morphological differentiation based on morphological characterisation and variation were carried out. The study was based on 864 Nile perch sampled from 25 different locations from different Lakes in the region and 10 morphological characters. Also determined were the length – weight relationships and condition factor of sampled Nile perch. The log transformed data of all sampled Nile perch were subjected to multivariate analysis, using ‘PAST’ statistical software. Findings showed that peduncle form and size, of all the variables used in this study, contributed most to the variance. The analysis clustered the Nile perch into two groups, which were found to be as characterised by earlier morphological description of this species and most probably are representatives of two distinct taxa of Nile perch in the East African waters. The LWRs and condition factor conformed to the fish isometric growth formula W = aLb with the value for the pooled data being W = 0.6664L0.3264. The existence of 2 morphs agrees with earlier taxonomists (Harrison, 1991; Ribbink, 1987; Bwathondi, 1985; Holden, 1967) who proposed that Nile perch exists in two populations – a bigger shallow water dwelling morph and a smaller deep open water dwelling morph. This calls for identification and mapping of the 2 populations in the different waters of East Africa that may require application of different management regimes.Keywords: Nile perch, taxa, morphological variation, East Africa

Evolution of Labeo victorianus predates the Pleistocene desiccation of Lake Victoria: evidence from mitochondrial DNA sequence variation

Geological data show that Lake Victoria dried out some 15 000 years ago. These data suggest that the entire faunal diversity within the lake has evolved since this time. However, mitochondrial DNA sequence diversity in the endemic cyprinid fish, Labeo victorianus, was high (24 haplotypes in 38 individuals; percentage sequence divergence of 0.74%), suggesting that the evolution of this species predates this Late Pleistocene climatological event. This finding is consistent with what has been reported earlier for cichlid fishes in the lake

East African pigs have a complex Indian, Far Eastern and Western ancestry

In this study, we have characterized the mitochondrial diversity of 81 swine from Uganda. Median-joining network analysis of D-loop sequences from these individuals and others characterized in previous studies allowed us to determine that Ugandan pigs cluster with populations from the West (Europe/North Africa), Far East and India. In addition, partial sequencing of the Y-chromosome UTY locus in 18 Ugandan domestic pigs revealed the segregation of a single HY1 lineage that has a cosmopolitan distribution. A Western and Far Eastern ancestry for East African pigs had been already reported, but this is the first study demonstrating an additional contribution from the Indian porcine gene pool. This result is consistent with the high frequency of zebuine alleles in cattle from East Africa. The geographic coordinates of East Africa, at the crossroads of many trading routes that, through the ages, linked Europe, Africa and Asia, might explain the rich and complex genetic heritage of livestock native to this area.We are greatly indebted to the Swedish International Development Agency (Sida) under the framework of Sida-Mak Bilateral Research Support Programme Phase 3 to the Post Doc program at the Directorate of Graduate and Research Training for the financial support (Grant No. 75007369, Swedish Research Links, contract number 348-2011-7380).Peer reviewe

Analysis of B. taurus and B. indicus admixture in Uganda as revealed by the Illumina BovineSNP50 Genotyping BeadChip

The NextGen project investigates disease resistance in indigenous Ugandan cattle. Since population structure and stratification may produce biased results, We have investigated the genomic structure of sampled animals genotyped with the BovineSNP50 Genotyping Beadchip. A total of 788 animals from 9 populations belonging to Ankole (crossbred between B. indicus and B. taurus), Zebu and Ankole-Zebu crosses have been sampled in 52 grid cells throughout the country (Table 1). We merged this data whit other 400 Italian Holstein Cattle, genotyped in the framework of SELMOL project to seek for a likely introgression of European B. taurus. The data were filtered with the following exclusion criteria: MAF < 0.01, genotype call rate (SNPs) < 0.95, genotype call rate (Animals) < 0.95. The resulting working dataset were composed of 43494 SNPs and 1188 animals. Hidden genetic structures were investigated by a Bayesian clustering approach with the ADMIXTURE software (Novembre et al. 2010). The software Admixture identified four ancestral genomic components. Three of them likely correspond to European taurine, African indicine and African taurine components (Figure 2). The fourth has a still unidentified origin (Yellow, Figure 2d). Most Ugandan individuals investigated have a remarkable level of admixture. Overall, about 20% of the Zebu genome is of African taurine origin, confirming previous data on the foundation of African Zebu. The European taurine (Blue, Figure 2) is a minor component of African genomes, rare in Zebu and evenly distributed in Ankole, other taurine subgroups and Ankole- Zebu crosses. Indicine and taurine components show a clear geographical structure, the former being predominant in north-eastern Uganda, and the latter in the south-west. Holstein Fresian introgression is spread mostly in south-western Uganda, while the fourth component is located in restricted geographical area in the East (Figure 3). The Ugandan cattle population is a complex admixture of African taurine (green in Figure 2) and zebuine (red) genomes, with a minor component of European origin (blue) and a rare but relevant contribution (yellow) from a still unidentified source. This complexity is to be accounted for in the following GWAS and selection signatures analyses planned within the NextGen project

African swine fever : update on Eastern, Central and Southern Africa

Control of African swine fever (ASF) in countries in Eastern, Central and Southern Africa (ECSA) is particularly complex owing to the presence of all three known epidemiological cycles of maintenance of the virus, namely an ancient sylvatic cycle involving the natural hosts and vectors of the disease as well as domestic cycles with and without involvement of natural vectors. While the situation is well documented in some of the countries, for others very little information is available. In spite of the unfavourable ASF situation, the pig population in the sub‐region has grown exponentially in recent decades and is likely to continue to grow in response to rapid urban growth resulting in increasing demand for animal protein by populations that are no longer engaged in livestock production. Better management of ASF will be essential to permit the pig sector to reach its full potential as a supplier of high quality protein and a source of income to improve livelihoods and create wealth. No vaccine is currently available and it is likely that, in the near future, the sub‐region will continue to rely on the implementation of preventive measures, based on the epidemiology of the disease, to avoid both the devastating losses that outbreaks can cause and the risk the sub‐region poses to other parts of Africa and the world. The current situation in the ECSA sub‐region is reviewed and gaps in knowledge are identified in order to support ongoing strategy development for managing ASF in endemic areas.LKD received funding from UK Biotechnology and Biological Sciences Research Council (BBSRC grant BBS/E/1/00007035. CM’s ASF research is funded by a Wellcome Trust Fellowship (Grant 105684/Z/14/Z) and the African Union Commission (Grant AURG‐II‐1‐196‐2016).http://wileyonlinelibrary.com/journal/tbed2020-07-01hj2019Veterinary Tropical Disease

Identification and distribution of Rhipicephalus microplus in selected high-cattle density districts in Uganda : signaling future demand for novel tick control approaches

DATA AVAILABITY STATEMENT: Data supporting the conclusion of this article are included within the article. The newly generated tick sequences were submitted to the GenBank database under the accession numbers (OR880375, OR880376, OR880377, OR880556, OR880557, OR880558, OR881483, OR881484 and OR881485). The datasets used and/or analyses during the preset study are available from the corresponding author upon reasonable request.BACKGROUND: Rhipicephalus (Boophilus) microplus (Canestrini, 1888), the Asian blue tick, is a highly invasive and adaptable ectoparasite. This tick species has successfully established itself in most regions of the world, with movement of cattle being a major driver for its spread. In the recent past, R. microplus ticks have been reported in three districts of Uganda. Information on its spread and distribution are vital in deepening our understanding of the ecological scenarios that lead to tick persistence and in the formulation of control strategies. This is especially important in the cattle-dense districts. METHODS: We randomly collected tick specimens from 1,461cattle spread across seven cattle dense districts located in the Central, Karamoja and West Nile regions of Uganda from January to September 2020. The ticks were identified using standard morpho-taxonomic keys and the R. microplus tick species identities were confirmed by sequencing of the ITS2 region, 12S rRNA and 16S rRNA genes and phylogenetic analyses. RESULTS: Adult ticks (n = 13,019) were collected from 1,461 cattle. Seventeen tick species were identified based on morpho-taxonomic keys and the majority (47.4%; n=6184) of these were R. appendiculatus. In total, 257 R. microplus ticks were found infesting cattle in 18 study sites in the districts of Amudat, Kaabong, Napak (Karamoja region) and Arua (West Nile region). The identity of R. microplus was confirmed using molecular technics. No R. microplus tick was recorded in the districts of Lyantonde and Nakaseke (Central region). Arua district accounted for 82.1% (n=211) of the R. microplus ticks recorded followed by Napak district at 16.3% (n=42), while Amudat and Kaabong districts accounted for 1.5% (n=4). Rhipicephalus microplus and R. decoloratus co-existed in 6 of the 13 study sites in Arua district, while in another 6 study sites, no R. decoloratus was recorded. In the Karamoja region districts R. decoloratus co-existed with R.microplus. Of the total 618 ticks belonging to four species of the subgenus Boophilus recorded in this study, R. decoloratus accounted for 50.04% (n=334), followed by R. microplus at 41.58% (n=257), R. geigyi at 2.75% (n=17) and R. annulatus at 1.61% (n=10). In the districts of Amudat, Kaabong and Napak, R. decoloratus was more dominant (76.1%; n=179) of the three Rhipicephalus (Boophilus) tick species recorded, followed by R. microplus (19.5%; n=46) and R. geigyi (4.2%; n=10). Contrariwise, R. microplus was more dominant (84%; n=211) in Arua district followed by R. decoloratus (10.7%; n=27), R. annulatus (3.9%; n=10) and R. geigyi (1.1%; n=3). Phylogenetic analyses of the ITS2 region, 12S rRNA and 16S rRNA genes revealed subgrouping of the obtained sequences with the previously published R. microplus sequences from other parts of the world. CONCLUSION: Rhipicephalus microplus ticks were found infesting cattle in four districts of Uganda. The inability to find R. decoloratus, an indigenous tick, from six sites in the district of Arua is suggestive of its replacement by R. microplus. Rhipicephalus microplus negatively affects livestock production, and therefore, there is a need to determine its distribution and to deepen the understanding of the ecological factors that lead to its spread and persistence in an area.The Germany Academic Exchange Service (DAAD), the Wellcome Trust, intermediate clinical fellowship and the Medical Research Council.https://bmcvetres.biomedcentral.com/Veterinary Tropical DiseasesSDG-02:Zero HungerSDG-03:Good heatlh and well-bein

Identification and distribution of Rhipicephalus microplus in selected high-cattle density districts in Uganda: signaling future demand for novel tick control approaches

Background: Rhipicephalus (Boophilus) microplus (Canestrini, 1888), the Asian blue tick, is a highly invasive and adaptable ectoparasite. This tick species has successfully established itself in most regions of the world, with movement of cattle being a major driver for its spread. In the recent past, R. microplus ticks have been reported in three districts of Uganda. Information on its spread and distribution are vital in deepening our understanding of the ecological scenarios that lead to tick persistence and in the formulation of control strategies. This is especially important in the cattle-dense districts. Methods: We randomly collected tick specimens from 1,461cattle spread across seven cattle dense districts located in the Central, Karamoja and West Nile regions of Uganda from January to September 2020. The ticks were identified using standard morpho-taxonomic keys and the R. microplus tick species identities were confirmed by sequencing of the ITS2 region, 12S rRNA and 16S rRNA genes and phylogenetic analyses. Results: Adult ticks (n = 13,019) were collected from 1,461 cattle. Seventeen tick species were identified based on morpho-taxonomic keys and the majority (47.4%; n=6184) of these were R. appendiculatus. In total, 257 R. microplus ticks were found infesting cattle in 18 study sites in the districts of Amudat, Kaabong, Napak (Karamoja region) and Arua (West Nile region). The identity of R. microplus was confirmed using molecular technics. No R. microplus tick was recorded in the districts of Lyantonde and Nakaseke (Central region). Arua district accounted for 82.1% (n=211) of the R. microplus ticks recorded followed by Napak district at 16.3% (n=42), while Amudat and Kaabong districts accounted for 1.5% (n=4). Rhipicephalus microplus and R. decoloratus co-existed in 6 of the 13 study sites in Arua district, while in another 6 study sites, no R. decoloratus was recorded. In the Karamoja region districts R. decoloratus co-existed with R.microplus. Of the total 618 ticks belonging to four species of the subgenus Boophilus recorded in this study, R. decoloratus accounted for 50.04% (n=334), followed by R. microplus at 41.58% (n=257), R. geigyi at 2.75% (n=17) and R. annulatus at 1.61% (n=10). In the districts of Amudat, Kaabong and Napak, R. decoloratus was more dominant (76.1%; n=179) of the three Rhipicephalus (Boophilus) tick species recorded, followed by R. microplus (19.5%; n=46) and R. geigyi (4.2%; n=10). Contrariwise, R. microplus was more dominant (84%; n=211) in Arua district followed by R. decoloratus (10.7%; n=27), R. annulatus (3.9%; n=10) and R. geigyi (1.1%; n=3). Phylogenetic analyses of the ITS2 region, 12S rRNA and 16S rRNA genes revealed subgrouping of the obtained sequences with the previously published R. microplus sequences from other parts of the world. Conclusion: Rhipicephalus microplus ticks were found infesting cattle in four districts of Uganda. The inability to find R. decoloratus, an indigenous tick, from six sites in the district of Arua is suggestive of its replacement by R. microplus. Rhipicephalus microplus negatively affects livestock production, and therefore, there is a need to determine its distribution and to deepen the understanding of the ecological factors that lead to its spread and persistence in an area